[Freesurfer] question about the vertex index?
Hello, I am wondering if there are 163842 vertices in fsaverage, will the vertex number be from 0 to 163841 or 1 to 163842 in the label file? Best, KIC ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Problem writing talairach.m3z in mri_ca_register
Hi Bruce, I run it on our local cluster and there is plenty of memory. Here is the memory print out from top: Mem: 18479108k total, 7724396k used, 10754712k free, 369152k buffers Swap: 72019344k total, 1475720k used, 70543624k free, 6322748k cached There is also plenty of disk space. Best, Lauge On Sun, Sep 18, 2011 at 04:52, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Lauge How much ram do yo have? Gzip need a lot Bruce On Sep 17, 2011, at 3:30 PM, Lauge Emil Borch Laurs S0rensen lau...@diku.dk wrote: Lauge The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] question about the vertex index?
0 to 163841 On Mon, Sep 19, 2011 at 3:44 PM, orangekic orange...@gmail.com wrote: Hello, I am wondering if there are 163842 vertices in fsaverage, will the vertex number be from 0 to 163841 or 1 to 163842 in the label file? Best, KIC ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] question about the vertex index?
Thanks for your answer. Furthermore, if I read the mri_preproc data (Group.mgh) by load_mgh in Matlab as below, Data=load_mgh(Group.mgh) then the size of Data =(163842,1,1,3) So, is the Data(2,1,1,3) represented the cortical thickness of the third subject (from fsgd file) on the second vertex (vertex number = 1)? Thomas Yeo Mon, 19 Sep 2011 02:45:50 -0700 0 to 163841 On Mon, Sep 19, 2011 at 3:44 PM, orangekic orange...@gmail.com wrote: Hello, I am wondering if there are 163842 vertices in fsaverage, will the vertex number be from 0 to 163841 or 1 to 163842 in the label file? Best, KIC ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tkmedit bus error
Thanks for the answers. I think the problem was the hard disk space, I can open it now in the views (tksurfer, tkmedit) Best regards, Carolina 2011/9/18 Gonzalo Rojas Costa gonzalo.rojas.co...@gmail.com Hi Carolina: And did you tested the tksurfer command ?... for example: tksurfer CORBIC_vol01 rh pial Sincerely, Gonzalo Rojas Costa Department of Radiology Clinica Las Condes Santiago Chile Message: 4 Date: Sun, 18 Sep 2011 10:25:26 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tkmedit bus error To: Carolina Valencia cvalen...@linkdx.com.co Cc: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Hi Carolina, does this happen every time? Can you run freeview on the volumes and see if it can display them properly? cheers Bruce On Thu, 15 Sep 2011, Carolina Valencia wrote: Hi FSusers I run recon-all in a patient without problems, but when I tried to view it in tkmedit, an error pops up. I appreciate your help! Best regards, Carolina recon-all -s CORBIC_vol01 finished without error at Tue Sep 13 12:42:43 COT 2011 done cvalencia-Precision-WorkStation-T3400:~ tkmedit CORBIC_vol01 brainmask.mgz -aux T1.mgz -surfs -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt Bus error cvalencia-Precision-WorkStation-T3400:~ tkmedit CORBIC_vol01 brainmask.mgz -aux T1.mgz -surfs -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt Bus error ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Is this normal when importing the annotations in tksurfer?
Hi, Doug As instructed in the testing page, I typed tksurfer bert rh pial and then went to File-Label-Import Annotation. The file rh.aparc.annot was selected to view cortical parcellation labels. Thanks Jerry From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, September 16, 2011 11:28 AM To: Chen, Xu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Is this normal when importing the annotations in tksurfer? Hi Jerry, what is the command you are running? I mean the full command line including the arguments. doug Chen, Xu wrote: Hi, Just installed FreeSurfer 5.1 ( stable ) to my 64 bit Ubuntu 10.04 LTS (kernel 2.6.32-33). Playing with it to test the Freesurfer installation. Everything seems OK when running tkmedit. However, a msg shown below pops up when I was trying to view cortical parcellation labels in tksurfer as instructed in the webpage of testingfreesurfer. .. Found embedded color table in annotation. 8600 vertices did not have an annotation! What does this message implicate? Could it be attributed to the data problem (e.g. the inconsistency of vertices between the annotation surface ) or my computer system? Is it normal to get it? Thanks a lot Jerry This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Is this normal when importing the annotations in tksurfer?
Hi Jerry were these just the locations on the medial wall around the corpus callosum that are non-cortical? cheers Bruce On Mon, 19 Sep 2011, Chen, Xu wrote: Hi, Doug As instructed in the testing page, I typed tksurfer bert rh pial and then went to File-Label-Import Annotation. The file rh.aparc.annot was selected to view cortical parcellation labels. Thanks Jerry From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, September 16, 2011 11:28 AM To: Chen, Xu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Is this normal when importing the annotations in tksurfer? Hi Jerry, what is the command you are running? I mean the full command line including the arguments. doug Chen, Xu wrote: Hi, Just installed FreeSurfer 5.1 ( stable ) to my 64 bit Ubuntu 10.04 LTS (kernel 2.6.32-33). Playing with it to test the Freesurfer installation. Everything seems OK when running tkmedit. However, a msg shown below pops up when I was trying to view cortical parcellation labels in tksurfer as instructed in the webpage of testingfreesurfer. .. Found embedded color table in annotation. 8600 vertices did not have an annotation! What does this message implicate? Could it be attributed to the data problem (e.g. the inconsistency of vertices between the annotation surface ) or my computer system? Is it normal to get it? Thanks a lot Jerry This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem writing talairach.m3z in mri_ca_register
On Mon, Sep 19, 2011 at 3:52 AM, Lauge Emil Borch Laurs S0rensen lau...@diku.dk wrote: I run it on our local cluster and there is plenty of memory. Here is the memory print out from top: Mem: 18479108k total, 7724396k used, 10754712k free, 369152k buffers Swap: 72019344k total, 1475720k used, 70543624k free, 6322748k cached There is also plenty of disk space. Are you sure that there aren't per process limits which are set lower than those? Richard ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] pial surface file format
You should already have them. In your $FREESURFER_HOME dir there is a sub-dir called 'matlab'. I believe 'read_surf.m' is what you are looking for. -Louis On Wed, 14 Sep 2011, Jeff Eriksen wrote: Super! Please tell me how to obtain the m-files. -Jeff On 9/14/11 6:49 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Yes, and we provide m files for reading them Cheers Bruce On Sep 14, 2011, at 9:46 PM, Jeff Eriksen eriks...@ohsu.edu wrote: I wish to extract the pial and GW surfaces from their surface files to manipulate in Matlab. As far as I can determine, these are the files lRh.white and lrh.pial. Can someone please confirm this, and also confirm that these are in the triangle surface file binary format? If this is all true, I can proceed to opening and reading the meshes. Thanks, -Jeff Eriksen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] question about the vertex index?
Yes doug orangekic wrote: Thanks for your answer. Furthermore, if I read the mri_preproc data (Group.mgh) by load_mgh in Matlab as below, Data=load_mgh(Group.mgh) then the size of Data =(163842,1,1,3) So, is the Data(2,1,1,3) represented the cortical thickness of the third subject (from fsgd file) on the second vertex (vertex number = 1)? Thomas Yeo Mon, 19 Sep 2011 02:45:50 -0700 0 to 163841 On Mon, Sep 19, 2011 at 3:44 PM, orangekic orange...@gmail.com mailto:orange...@gmail.com wrote: Hello, I am wondering if there are 163842 vertices in fsaverage, will the vertex number be from 0 to 163841 or 1 to 163842 in the label file? Best, KIC ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Is this normal when importing the annotations in tksurfer?
Yes, that message is that the medial all vertices do not have a label. This is normal and nothing to worry about. doug Bruce Fischl wrote: Hi Jerry were these just the locations on the medial wall around the corpus callosum that are non-cortical? cheers Bruce On Mon, 19 Sep 2011, Chen, Xu wrote: Hi, Doug As instructed in the testing page, I typed tksurfer bert rh pial and then went to File-Label-Import Annotation. The file rh.aparc.annot was selected to view cortical parcellation labels. Thanks Jerry From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, September 16, 2011 11:28 AM To: Chen, Xu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Is this normal when importing the annotations in tksurfer? Hi Jerry, what is the command you are running? I mean the full command line including the arguments. doug Chen, Xu wrote: Hi, Just installed FreeSurfer 5.1 ( stable ) to my 64 bit Ubuntu 10.04 LTS (kernel 2.6.32-33). Playing with it to test the Freesurfer installation. Everything seems OK when running tkmedit. However, a msg shown below pops up when I was trying to view cortical parcellation labels in tksurfer as instructed in the webpage of testingfreesurfer. .. Found embedded color table in annotation. 8600 vertices did not have an annotation! What does this message implicate? Could it be attributed to the data problem (e.g. the inconsistency of vertices between the annotation surface ) or my computer system? Is it normal to get it? Thanks a lot Jerry This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkmedit bus error
Hi Carolina: Is it possible, but in my case when the hard disk is full at the moment of the processing, I got a fatal error from recon-all command... Sincerely, Gonzalo Rojas Costa El 19-09-2011 9:53, Carolina Valencia escribió: Thanks for the answers. I think the problem was the hard disk space, I can open it now in the views (tksurfer, tkmedit) Best regards, Carolina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] ICV differences from version 5.0 to 5.1
in v5.1, the talairach stage was moved to precede the nu_correct stage, so that creation of nu.mgz can benefit from usage of the talairach.xfm. this means that the talairach stage uses orig.mgz as input instead of nu.mgz (the nu_correct'd image). in looking at your talairach images, they seem good enough for freesurfer purposes, but clearly are not as good as v5.0. they seems sufficient for ICV as long as ICV is used as normalizer for, say, hippocampal volume, in a group study. the freesurfer ICV is not a very accurate absolute measure (see wiki on how its calculated). i suppose we could run the talairach stage again after nu.mgz is created, since the talairach stage only takes a couple minutes. n. On Mon, 2011-09-19 at 10:25 -0500, Koller, Jonathan wrote: Hi Ed and freesurfer folks, Thanks for your reply, but I think that the ICV is computed from talairach.xfm (see lines 3261-3266 in the current recon-all), which is actually computed before any normalization. If you look at file times, talairach.xfm (in the mri/transforms/ directory) is created right after orig.mgz, and before nu.mgz. The input for the 12-parameter talairach registration is the orig.mgz image (converted to analyze, and then 4dfp format). Is this not the case? Thanks, Jon From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Ed Gronenschild Sent: Saturday, September 17, 2011 2:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ICV differences from version 5.0 to 5.1 Jon, The reason is that already in one step earlier in the pipeline, the nu-correct stage, a difference arises. See thread on Differences in nu.mgz between v5.0.0 and v5.1.0 Cheers, Ed Hi, We have noticed differences in Talairach registration (and therefore ICV estimates) in some of our subjects from version 5.0 to version 5.1. Please see the attached document. There are 4 subjects, each row represents the same subject, same input images, same recon-all options (-all) between versions. The bottom of the second page has a table with the ICV values for these subjects across versions. Have there been any changes to the Talairach registration step from 5.0 to 5.1 that would account for these differences? Thanks, Jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Is this normal when importing the annotations in tksurfer?
Thanks for the clarification! Cheers Jerry From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, September 19, 2011 10:15 AM To: Bruce Fischl Cc: Chen, Xu; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Is this normal when importing the annotations in tksurfer? Yes, that message is that the medial all vertices do not have a label. This is normal and nothing to worry about. doug Bruce Fischl wrote: Hi Jerry were these just the locations on the medial wall around the corpus callosum that are non-cortical? cheers Bruce On Mon, 19 Sep 2011, Chen, Xu wrote: Hi, Doug As instructed in the testing page, I typed tksurfer bert rh pial and then went to File-Label-Import Annotation. The file rh.aparc.annot was selected to view cortical parcellation labels. Thanks Jerry From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, September 16, 2011 11:28 AM To: Chen, Xu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Is this normal when importing the annotations in tksurfer? Hi Jerry, what is the command you are running? I mean the full command line including the arguments. doug Chen, Xu wrote: Hi, Just installed FreeSurfer 5.1 ( stable ) to my 64 bit Ubuntu 10.04 LTS (kernel 2.6.32-33). Playing with it to test the Freesurfer installation. Everything seems OK when running tkmedit. However, a msg shown below pops up when I was trying to view cortical parcellation labels in tksurfer as instructed in the webpage of testingfreesurfer. .. Found embedded color table in annotation. 8600 vertices did not have an annotation! What does this message implicate? Could it be attributed to the data problem (e.g. the inconsistency of vertices between the annotation surface ) or my computer system? Is it normal to get it? Thanks a lot Jerry This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mris_calc problem
I have ran into a problem with mris_calc using Freesurfer 5.1 on Mac OS Leopard. When running long_mris_slopes I am getting this error; ERROR 1 : mris_calc compute sym. pct. change (spc) problem? It seems to running properly until it hits; mris_calc -o /Volumes/larry/cluster_results/1007base3/surf/lh.long.thickness-spc.fwhm0.mgh ./tmp-1007base3_lh_thickness_PENQ8v/beta1.mgh div ./tmp-1007base3_lh_thickness_PENQ8v/beta0.mgh The ./tmp files do exist whern mris_calc is called. I have seen on the Wiki that a fixed version of mris_calc is available for Centos. If you think I could be running into the same problem, is a fix available for Leopard? Thanks, Kevin Department of Neurology University of Wisconsin-Madison ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mris_calc problem
The problem was a bug related to a buffer overflow on the string lengths of command line arguments. Basically, filename/directory names that were too long triggered it. Nick might know if a newer Mac build is available. In the meantime, you can try re-running the command with shorter file/dir names: 1. Copy your inputs, beta1.mgh and beta2.mgh to some dir, say ~/tmp 2. Run something shorter like: cd ~/tmp mris_calc -o beta_out.mgh beta1.mgh div beta0.mgh mv beta_out.mgh /Volumes/larry/cluster_results/1007base3/surf/lh.long.thickness-spc.fwhm0.mgh On 9/19/11 15:47 , Dabbs (Kevin) wrote: I have ran into a problem with mris_calc using Freesurfer 5.1 on Mac OS Leopard. When running long_mris_slopes I am getting this error; ERROR 1 : mris_calc compute sym. pct. change (spc) problem? It seems to running properly until it hits; mris_calc -o /Volumes/larry/cluster_results/1007base3/surf/lh.long.thickness-spc.fwhm0.mgh ./tmp-1007base3_lh_thickness_PENQ8v/beta1.mgh div ./tmp-1007base3_lh_thickness_PENQ8v/beta0.mgh The ./tmp files do exist whern mris_calc is called. I have seen on the Wiki that a fixed version of mris_calc is available for Centos. If you think I could be running into the same problem, is a fix available for Leopard? Thanks, Kevin Department of Neurology University of Wisconsin-Madison ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mris_calc problem
i've put the updated mris_calc for macos leopard here: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-intel/ On Mon, 2011-09-19 at 14:47 -0500, Dabbs (Kevin) wrote: I have ran into a problem with mris_calc using Freesurfer 5.1 on Mac OS Leopard. When running long_mris_slopes I am getting this error; ERROR 1 : mris_calc compute sym. pct. change (spc) problem? It seems to running properly until it hits; mris_calc -o /Volumes/larry/cluster_results/1007base3/surf/lh.long.thickness-spc.fwhm0.mgh ./tmp-1007base3_lh_thickness_PENQ8v/beta1.mgh div ./tmp-1007base3_lh_thickness_PENQ8v/beta0.mgh The ./tmp files do exist whern mris_calc is called. I have seen on the Wiki that a fixed version of mris_calc is available for Centos. If you think I could be running into the same problem, is a fix available for Leopard? Thanks, Kevin Department of Neurology University of Wisconsin-Madison ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mris_calc problem
Hello Freesurfer's If tkmedit shows the T1 image in radiological convention, then what convention does the surface reconstruction follow? Please advice! Regards, Manish Dalwani ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Laterality Issue!
Hello Freesurfer's If tkmedit shows the T1 image in radiological convention, then what convention does the surface reconstruction follow? Please advice! Regards, Manish Dalwani P.s. I sent this email out earlier with the wrong subject name... ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Laterality Issue!
There is no convention for the surfaces. If it is labeled lh, then it is left hemi, etc. doug Dalwani, Manish wrote: Hello Freesurfer's If tkmedit shows the T1 image in radiological convention, then what convention does the surface reconstruction follow? Please advice! Regards, Manish Dalwani P.s. I sent this email out earlier with the wrong subject name... ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] register.dat Matrix Conventions
Hello, I was wondering what orientation conventions are used when calculating the affine transformation matrix in register.dat. For an example, I'll use the data from subject 101 of the fsfast tutorial. According to mri_info, the functional volume is in LPS orientation, and the processed anatomical volume (T1.mgz) is in LIA orientation. Does the matrix in register.dat convert from the functional LPS orientation to the anatomical LIA orientation, or does the matrix assume these volumes are already transformed in some other way? Thanks, Clark ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
